Question: Can I change the sequencing length of the i5 and i7 indices?
Answer: The final configuration of a single cell ATAC library is the following:
The i5 and i7 reads are necessary to identify the 10x Barcode and Sample Index, respectively.
The 10x Barcode is necessary to trace the read back to the individual nucleus it came from, as all fragments within each nucleus are tagged with the same 10x Barcode. If this read is shortened, cell-specific information will be lost and Cell Ranger ATAC will be unable to complete successfully.
The Sample Index is necessary to distinguish between pooled samples for sequencing and is used for demultiplexing. If this read is shortened, it will be difficult to demultiplex pooled samples. If only one sample is being sequenced in one lane, the impact of a shorter i7 read may be diminished.
It's best practice to adhere to the recommended sequencing lengths.
Product: Single Cell ATAC